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  • An ionbot search requires the selection of a target Protein Database and a machine specific MS2 Fragmentation Method (currently HCD only).
  • Up to four different potential peptide modifications (expected variable modifications) can be considered during the search (expected fixed modifications are not limited to a maximum).
    The ionbot engine considers all selected fixed modifications combined with up to two of the expected variable modifications in each candidate peptide.
  • The ionbot engine performs an Extended Modification Search by default.
    This means that ionbot considers one more unexpected modification (in addition to the maximum two expected variable modifications selected from the list of four different modifications) for each candidate peptide from the list of modifications provided by the unimod.org repository.
    To disable extended modification search you need to unmark the “Enable Extended Modifications Search” box.
A note on extended modification searching.

It considers one more unexpected modification (including an amino acid mutation) for each candidate peptide. This is in addition to the maximum two expected variable modifications selected from the list of four different modifications.

The extended modifications considered by ionbot are listed in the table below (amino acid mutations not listed):


id modification targets mass
1 Acetyl T,N-term,S,C,K,Y,H,R 42.010565
2 Amidated C-term -0.984016
3 Biotin N-term,K 226.077598
4 Carbamidomethyl Y,T,S,E,D,H,N-term,K,C,U,M 57.021464
5 Carbamyl Y,T,S,M,C,R,N-term,K 43.005814
6 Carboxymethyl N-term,K,C,W,U 58.005479
7 Deamidated Q,R,N,F 0.984016
10 Met->Hse M -29.992806
11 Met->Hsl M -48.003371
17 NIPCAM C 99.068414
20 PEO-Iodoacetyl-LC-Biotin C 414.193691
21 Phospho C,H,D,Y,T,S,R 79.966331
23 Dehydrated D,Y,T,S,N,Q,C -18.010565
24 Propionamide C,K,N-term 71.037114
25 Pyridylacetyl N-term,K 119.037114
26 Pyro-carbamidomethyl C 39.994915
27 Glu->pyro-Glu E -18.010565
28 Gln->pyro-Glu Q -17.026549
29 SMA N-term,K 127.063329
30 Cation:Na D,C-term,E 21.981943
31 Pyridylethyl C 105.057849
34 Methyl E,D,C-term,N-term,L,I,R,Q,N,K,H,C,S,T 14.01565
35 Oxidation T,E,S,Q,L,I,U,G,W,C,H,V,R,M,Y,F,P,N,K,D 15.994915
36 Dimethyl N-term,P,N,K,R 28.0313
37 Trimethyl A,R,K 42.04695
39 Methylthio C,N,D,K,N-term 45.987721
40 Sulfo S,T,Y,C 79.956815
42 Lipoyl K 188.032956
44 Farnesyl C 204.187801
45 Myristoyl C,K,G 210.198366
46 PyridoxalPhosphate K 229.014009
47 Palmitoyl T,S,K,C,N-term 238.229666
48 GeranylGeranyl C 272.250401
49 Phosphopantetheine S 340.085794
50 FAD Y,H,C 783.141486
51 Tripalmitate C 788.725777
52 Guanidinyl K,N-term 42.021798
53 HNE K,H,C,A,L 156.11503
55 Glutathione C 305.068156
58 Propionyl N-term,K,S,T 56.026215
64 Succinyl N-term,K 100.016044
357 probiotinhydrazide P 258.115047
359 Pro->pyro-Glu P 13.979265
350 Trp->Hydroxykynurenin W 19.989829
368 Cys->Dha C -33.987721
344 Arg->GluSA R -43.053433
345 Trioxidation Y,W,C,F 47.984744
89 Iminobiotin N-term,K 225.093583
92 NHS-LC-Biotin N-term,K 339.161662
93 EDT-maleimide-PEO-biotin T,S 601.206246
353 Lysbiotinhydrazide K 241.088497
354 Nitro Y,W,F 44.985078
351 Trp->Kynurenin W 3.994915
352 Lys->Allysine K -1.031634
107 FormylMet N-term 159.035399
108 Nethylmaleimide C 125.047679
112 OxLysBiotinRed K 354.172562
119 IBTP C 316.138088
113 OxLysBiotin K 352.156911
114 OxProBiotinRed P 371.199111
115 OxProBiotin P 369.183461
116 OxArgBiotin R 310.135113
117 OxArgBiotinRed R 312.150763
118 EDT-iodoacetyl-PEO-biotin T,S 490.174218
121 GG N-term 114.042927
122 Formyl N-term,T,K,S 27.994915
530 Cation:K C-term,E,D 37.955882
126 Xlink:DTSSP[88 N-term,K 87.998285
1897 Xlink:EGS[226 K,N-term 226.047738
127 Fluoro A 17.990578
128 Fluorescein C 387.074287
129 Iodo H,Y 125.896648
130 Diiodo Y,H 251.793296
131 Triiodo Y 377.689944
134 Myristoleyl G 208.182715
360 Pro->Pyrrolidinone P -30.010565
135 Myristoyl+Delta:H(-4) G 206.167065
139 Dansyl N-term,K 233.051049
141 Amidine N-term,K 41.026549
171 NBS:13C(6) W 159.008578
172 NBS W 152.988449
195 QAT C 171.149738
327 Delta:H(4)C(2)O(-1)S(1) S 44.008456
178 DAET T,S 87.050655
369 Pro->Pyrrolidone P -27.994915
186 HPG R 132.021129
187 2HPG R 282.052824
194 AccQTag N-term,K 170.048013
197 EQAT C 184.157563
200 Ethanedithiol T,S 75.980527
206 Delta:H(4)C(3)O(1) R 56.026215
340 Bromo F,H,W,Y 77.910511
342 Amino Y 15.010899
343 Argbiotinhydrazide R 199.066699
261 SPITC K,N-term 214.971084
270 Cytopiloyne Y,S,R,P,N-term,K,C 362.136553
271 Cytopiloyne+water Y,T,S,R,N-term,K,C 380.147118
264 PET T,S 121.035005
272 CAF N-term 135.983029
1905 Xlink:BS2G[96 N-term,K 96.021129
275 Nitrosyl C 28.990164
276 AEBS Y,S,N-term,K,H 183.035399
278 Ethanolyl K,C,R 44.026215
371 HMVK C 86.036779
280 Ethyl C-term,N-term,E,K,D 28.0313
281 CoenzymeA C 765.09956
528 Methyl+Deamidated Q,N 14.999666
529 Delta:H(5)C(2) P 29.039125
286 SulfanilicAcid:13C(6) E,D,C-term 161.024228
289 Biotin-PEO-Amine D,C-term,E 356.188212
288 Trp->Oxolactone W 13.979265
290 Biotin-HPDP C 428.191582
291 Delta:Hg(1) C 201.970617
292 IodoU-AMP Y,W,F 322.020217
293 CAMthiopropanoyl N-term,K 145.019749
294 IED-Biotin C 326.141261
299 Carboxy E,D,K,W,M 43.989829
301 Bromobimane C 190.074228
302 Menadione K,C 170.036779
303 DeStreak C 75.998285
312 Cysteinyl C 119.004099
313 Lys-loss K -128.094963
314 Nmethylmaleimide K,C 111.032028
494 CyDye-Cy3 C 672.298156
316 DimethylpyrroleAdduct K 78.04695
318 Delta:H(2)C(5) K 62.01565
319 Delta:H(2)C(3)O(1) K,R 54.010565
320 Nethylmaleimide+water K,C 143.058243
323 Xlink:B10621 C 713.093079
324 Xlink:DTBP[87 N-term,K 87.01427
325 FP-Biotin K,T,Y,S 572.316129
332 Thiophos-S-S-biotin Y,T,S 525.142894
333 Can-FP-biotin T,Y,S 447.195679
335 HNE+Delta:H(2) K,H,C 158.13068
361 Thrbiotinhydrazide T 240.104482
337 Methylamine T,S 13.031634
362 Diisopropylphosphate K,Y,T,S,N-term 164.060231
363 Isopropylphospho Y,T,S 122.013281
893 CarbamidomethylDTT C 209.018035
372 Arg->Orn R -42.021798
531 Cation:Cu[I C-term,E,D,H 61.921774
374 Dehydro C -1.007825
375 Diphthamide H 142.110613
376 Hydroxyfarnesyl C 220.182715
377 Diacylglycerol C 576.511761
378 Carboxyethyl K,H 72.021129
379 Hypusine K 87.068414
380 Retinylidene K 266.203451
381 Lys->AminoadipicAcid K 14.96328
382 Cys->PyruvicAcid C -33.003705
385 Ammonia-loss C,S,T,N -17.026549
387 Phycocyanobilin C 586.279135
388 Phycoerythrobilin C 588.294785
389 Phytochromobilin C 584.263485
390 Heme H,C 616.177295
391 Molybdopterin C 521.884073
392 Quinone W,Y 29.974179
394 GPIanchor C-term 123.00853
395 PhosphoribosyldephosphoCoA S 881.146904
396 GlycerylPE E 197.04531
397 Triiodothyronine Y 469.716159
398 Thyroxine Y 595.612807
400 Tyr->Dha Y -94.041865
401 Didehydro S,Y,T,K -2.01565
402 Cys->Oxoalanine C -17.992806
403 Ser->LacticAcid S -15.010899
451 GluGlu E,C-term 258.085186
405 Phosphoadenosine H,T,K,Y 329.05252
450 Glu E,C-term 129.042593
407 Hydroxycinnamyl C 146.036779
409 FMNH H,C 454.088965
410 Archaeol C 634.662782
411 Phenylisocyanate N-term 119.037114
412 Phenylisocyanate:2H(5) N-term 124.068498
413 Phosphoguanosine H,K 345.047435
414 Hydroxymethyl N 30.010565
415 MolybdopterinGD+Delta:S(-1)Se(1) C 1620.930224
416 Dipyrrolylmethanemethyl C 418.137616
417 PhosphoUridine H,Y 306.025302
419 Glycerophospho S 154.00311
420 Carboxy->Thiocarboxy G 15.977156
421 Sulfide D,C,W 31.972071
422 PyruvicAcidIminyl K,V,C 70.005479
423 Delta:Se(1) C 79.91652
424 MolybdopterinGD D,C,U 1572.985775
425 Dioxidation U,C,W,Y,F,M,K,R,P,E,I,L,V 31.989829
426 Octanoyl T,S,C 126.104465
431 Palmitoleyl C,S,T 236.214016
432 Cholesterol C-term 368.344302
433 Didehydroretinylidene K 264.187801
434 CHDH D 294.183109
435 Methylpyrroline K 109.052764
436 Hydroxyheme E 614.161645
437 MicrocinC7 C-term 386.110369
438 Cyano C 24.995249
439 Diironsubcluster C 342.786916
440 Amidino C 42.021798
442 FMN S,T 438.094051
443 FMNC C 456.104615
444 CuSMo C 922.834855
445 Hydroxytrimethyl K 59.04969
447 Deoxy T,D,S -15.994915
448 Microcin C-term 831.197041
449 Decanoyl T,S 154.135765
452 GluGluGlu C-term,E 387.127779
453 GluGluGluGlu C-term,E 516.170373
455 Xlink:DMP[154 N-term,K 154.110613
457 NDA N-term,K 175.042199
464 SPITC:13C(6) N-term,K 220.991213
478 FTC S,R,P,K,C 421.073241
472 AEC-MAEC T,S 59.019355
495 CyDye-Cy5 C 684.298156
488 DHP C 118.065674
500 Nmethylmaleimide+water C 129.042593
501 PyMIC N-term 134.048013
503 LG-lactam-K N-term,K 332.19876
519 BisANS K 594.091928
520 Piperidine N-term,K 68.0626
518 Diethyl N-term,K 56.0626
504 LG-Hlactam-K N-term,K 348.193674
513 C8-QAT N-term,K 227.224915
505 LG-lactam-R R 290.176961
1036 Withaferin C 470.266839
1037 Biotin:Thermo-88317 S,Y 443.291294
506 LG-Hlactam-R R 306.171876
522 Maleimide-PEO2-Biotin C 525.225719
523 Sulfo-NHS-LC-LC-Biotin N-term,K 452.245726
515 FNEM C 427.069202
514 PropylNAGthiazoline C 232.064354
526 Dethiomethyl M -48.003371
534 Dibromo Y 155.821022
535 LRGG K 383.228103
684 BDMAPP W,Y,N-term,K,H 253.010225
685 NA-LNO2 C,H 325.225309
686 NA-OA-NO2 C,H 327.240959
894 CarboxymethylDTT C 210.00205
720 HNE-Delta:H(2)O K,H,C 138.104465
721 4-ONE K,H,C 154.09938
723 O-Dimethylphosphate Y,T,S 107.997631
724 O-Methylphosphate Y,T,S 93.981981
725 Diethylphosphate N-term,H,C,K,Y,T,S 136.028931
726 Ethylphosphate N-term,K,Y,T,S 107.997631
727 O-pinacolylmethylphosphonate T,S,K,Y,H 162.080967
728 Methylphosphonate Y,T,S 77.987066
729 O-Isopropylmethylphosphonate Y,T,S 120.034017
735 BEMAD_ST T,S 136.001656
734 Ethanolamine D,C-term,E,C 43.042199
736 BEMAD_C C 120.0245
739 TMT N-term,K,H,S,T 224.152478
744 NO_SMX_SEMD C 252.044287
743 4-ONE+Delta:H(-2)O(-1) K,H,C 136.088815
745 NO_SMX_SMCT C 268.039202
746 NO_SMX_SIMD C 267.031377
747 Malonyl C,S,K 86.000394
748 3sulfo N-term 183.983029
751 TNBS N-term,K 210.986535
774 Biotin-phenacyl C,H,S 626.263502
771 lapachenole C 240.11503
773 maleimide K,C 97.016378
765 Met-loss M -131.040485
766 Met-loss+Acetyl M -89.02992
767 Menadione-HQ K,C 172.05243
775 Carboxymethyl:13C(2) C 60.012189
776 NEM:2H(5) C 130.079062
822 Gly-loss+Amide G -58.005479
827 TMPP-Ac N-term 572.181134
837 Arg->Npo R 80.985078
801 Pentylamine Q 85.089149
800 Biotin:Thermo-21345 Q 311.166748
830 Dihydroxyimidazolidine R 72.021129
825 Xlink:DFDNB N,Q,R,K 163.985807
821 Cy3b-maleimide C 682.24612
824 Xlink:BMOE C 220.048407
811 Biotin:Thermo-21360 C-term 487.246455
849 cGMP S,C 343.031785
851 cGMP+RMP-loss C,S 150.041585
848 Arg2PG R 266.057909
853 Label:2H(4)+GG K 118.068034
1420 spermine Q 185.189198
890 DyLight-maleimide C 940.1999
891 Methyl-PEO12-Maleimide C 710.383719
887 MDCC C 383.148121
884 Biotin:Thermo-21325 K 695.310118
885 Label:13C(1)2H(3)+Oxidation M 20.0171
878 Bodipy C 414.167478
895 Biotin-PEG-PRA M 578.317646
898 pyrophospho T,S 159.932662
901 4AcAllylGal C 372.142033
902 DimethylArsino C 103.960719
903 Lys->CamCys K 31.935685
904 Phe->CamCys F 12.962234
905 Leu->MetOx L 33.951335
906 Lys->MetOx K 18.940436
908 Xlink:SMCC[321 C 321.205242
911 MTSL C 184.07961
912 HNE-BAHAH H,C,K 511.319226
915 Ethoxyformyl H 72.021129
914 Methylmalonylation S 100.016044
938 AROD C 820.336015
939 Cys->methylaminoAla C -2.945522
940 Cys->ethylaminoAla C 11.070128
926 ethylamino S,T 27.047285
928 MercaptoEthanol S,T 60.003371
935 Atto495Maleimide C 474.250515
934 AMTzHexNAc2 T,S,N 502.202341
931 Ethyl+Deamidated Q,N 29.015316
936 Chlorination W,Y 33.961028
937 dichlorination C,Y 67.922055
941 DNPS C,W 198.981352
943 DimethylamineGMBS C 267.158292
946 LG-anhydrolactam N-term,K 314.188195
947 LG-pyrrole N-term,K 316.203845
948 LG-anhyropyrrole N-term,K 298.19328
949 3-deoxyglucosone R 144.042259
950 Cation:Li D,E,C-term 6.008178
951 Cation:Ca[II C-term,E,D 37.946941
952 Cation:Fe[II D,E,C-term 53.919289
953 Cation:Ni[II D,E,C-term 55.919696
954 Cation:Zn[II C-term,E,D,H 61.913495
955 Cation:Ag D,E,C-term 105.897267
956 Cation:Mg[II D,E,C-term 21.969392
957 2-succinyl C 116.010959
958 Propargylamine D,C-term,E 37.031634
959 Phosphopropargyl T,Y,S 116.997965
975 Chlorpyrifos S,T,Y 153.013912
978 BITC N-term,K,C 149.02992
977 Carbofuran S 58.029289
979 PEITC N-term,K,C 163.04557
967 thioacylPA K 159.035399
971 maleimide3 K,C 969.366232
972 maleimide5 K,C 1293.471879
973 Puromycin C-term 453.212452
984 cysTMT C 299.166748
991 ISD_z+2_ion N-term -15.010899
989 Ammonium E,D,C-term 17.026549
993 Biotin:Sigma-B1267 C 449.17329
997 sulfo+amino Y 94.967714
1000 AHA-Alkyne M 107.077339
1001 AHA-Alkyne-KDDDD M 695.280074
1002 EGCG1 C 456.069261
1003 EGCG2 C 287.055563
1009 Thiazolidine W,Y,H,R,K,N-term,C,F 12.0
1010 DEDGFLYMVYASQETFG K 1970.824411
1012 Biotin:Invitrogen-M1602 C 523.210069
1020 Xlink:DSS[156 K,N-term 156.078644
1017 DMPO H,Y,C 111.068414
1014 glycidamide K,N-term 87.032028
1021 Xlink:EGS[244 N-term,K 244.058303
1022 Xlink:DST[132 N-term,K 132.005873
1023 Xlink:DTSSP[192 N-term,K 191.991486
1024 Xlink:SMCC[237 C,K,N-term 237.100108
1032 2-nitrobenzyl Y 135.032028
1027 Xlink:DMP[140 N-term,K 140.094963
1028 Xlink:EGS[115 N-term,K 115.026943
1034 Cys->SecNEM:2H(5) C 178.023511
1035 Thiadiazole C 174.025169
1031 Biotin:Thermo-88310 K 196.121178
1038 TAMRA-FP Y,S 659.312423
1039 Biotin:Thermo-21901+H2O C 543.236284
1041 Deoxyhypusine Q,K 71.073499
1042 Acetyldeoxyhypusine K 97.089149
1043 Acetylhypusine K 113.084064
1249 AHA-SS M 195.075625
1250 AHA-SS_CAM M 252.097088
1251 Biotin:Thermo-33033 N-term 548.223945
1252 Biotin:Thermo-33033-H N-term 546.208295
1253 2-monomethylsuccinyl C 130.026609
1254 Saligenin H,K 106.041865
1255 Cresylphosphate R,S,T,Y,K,H 170.013281
1256 CresylSaligeninPhosphate R,S,T,Y,K,H 276.055146
1257 Ub-Br2 C 100.063663
1258 Ub-VME C 173.092617
1260 Ub-amide C 196.108602
1261 Ub-fluorescein C 597.209772
1262 2-dimethylsuccinyl C 144.042259
1264 pupylation K 243.085521
1271 HCysteinyl C 133.019749
1276 UgiJoullie E,D 1106.48935
1270 HCysThiolactone K 117.024835
1282 UgiJoullieProGly D,E 154.074228
1277 Dipyridyl C 225.090212
1278 Furan Y 66.010565
1279 Difuran Y 132.021129
1281 BMP-piperidinol C,M 263.131014
1283 UgiJoullieProGlyProGly D,E 308.148455
1289 Butyryl K 70.041865
1290 Dicarbamidomethyl K,H,C,R,N-term 114.042927
1305 Propyl D,K,N-term,E,C-term 42.04695
1310 Propiophenone C,W,T,S,R,K,H 132.057515
1345 PS_Hapten H,C,K 120.021129
1348 Cy3-maleimide C 753.262796
1312 Delta:H(6)C(3)O(1) N-term,K,H,C 58.041865
1313 Delta:H(8)C(6)O(1) N-term,K 96.057515
1314 biotinAcrolein298 H,K,N-term,C 298.146347
1315 MM-diphenylpentanone C 265.146664
1317 EHD-diphenylpentanone M,C 266.13068
1349 benzylguanidine K 132.068748
1350 CarboxymethylDMAP N-term 162.079313
1320 Biotin:Thermo-21901+2H2O C 561.246849
1887 Xlink:BuUrBu[213 K,N-term 213.111341
1330 bisANS-sulfonates S,T,K 437.201774
1331 DNCB_hapten Y,H,K,C 166.001457
1326 NEMsulfur C 157.019749
1327 SulfurDioxide C 63.9619
1328 NEMsulfurWater C 175.030314
1389 HN3_mustard C,H,K 131.094629
1387 3-phosphoglyceryl K 167.982375
1388 HN2_mustard H,K,C 101.084064
1358 NEM:2H(5)+H2O C 148.089627
1363 Crotonyl K 68.026215
1364 O-Et-N-diMePhospho S 135.044916
1365 N-dimethylphosphate S 107.013615
1356 phosphoRibosyl E,R,D 212.00859
1355 azole C,S -20.026215
1340 Biotin:Thermo-21911 C 921.461652
1341 iodoTMT K,H,E,D,C 324.216141
1342 iodoTMT6plex K,H,E,D,C 329.226595
1344 Phosphogluconoylation N-term,K 258.014069
1380 methylsulfonylethyl K,H,C 106.00885
1381 ethylsulfonylethyl H,C,K 120.0245
1382 phenylsulfonylethyl C 168.0245
1383 PyridoxalPhosphateH2 K 231.02966
1384 Homocysteic_acid M 33.969094
1385 Hydroxamic_acid E,D 15.010899
1390 Oxidation+NEM C 141.042593
1391 NHS-fluorescein K 471.131802
1397 Iodoacetanilide K,C,N-term 133.052764
1398 Iodoacetanilide:13C(6) K,C,N-term 139.072893
1399 Dap-DSP K 364.076278
1405 EEEDVIEVYQEQTGG K 1705.73189
1406 EDEDTIDVFQQQTGG K 1662.700924
1419 15N-oxobutanoic S,C,T -18.023584
1421 spermidine Q 128.131349
1423 Biotin:Thermo-21330 N-term,K 473.219571
1789 Xlink:DSS[155 N-term,K 155.094629
1799 NQIGG K 469.228496
1801 Fluorescein-tyramine Y 493.116152
1839 betaFNA C,K 454.210387
1831 Tris N 104.071154
1830 Biotin-tyramide Y 361.146012
1829 LRGG+dimethyl K 411.259403
1824 GEE Q 86.036779
1826 Glu->pyro-Glu+Methyl E -3.994915
1827 Glu->pyro-Glu+Methyl:2H(2)13C(1) E -0.979006
1828 LRGG+methyl K 397.243753
1832 IASD C 452.034807
1841 Biotin:Thermo-21328 K,N-term 389.090154
1843 PhosphoCytidine Y,T,S 305.041287
1845 AzidoF F 41.001397
1846 Dimethylaminoethyl C 71.073499
1848 Gluratylation K 114.031694
1849 2-hydroxyisobutyrylation K 86.036779
1868 MeMePhosphorothioate S 107.979873
1870 Cation:Fe[III D,E,C-term 52.911464
1871 DTT C 151.996571
1878 Xlink:DSSO[176 K,N-term 176.01433
1873 MesitylOxide K,H,N-term 98.073165
1877 Xlink:DSS[259 K,N-term 259.141973
1875 methylol Y,W,K 30.010565
1879 Xlink:DSSO[175 K,N-term 175.030314
1880 Xlink:DSSO[279 K,N-term 279.077658
1881 Xlink:DSSO[54 N-term,K 54.010565
1882 Xlink:DSSO[86 K,N-term 85.982635
1883 Xlink:DSSO[104 K,N-term 103.9932
1885 Xlink:BuUrBu[111 K,N-term 111.032028
1886 Xlink:BuUrBu[85 K,N-term 85.052764
1888 Xlink:BuUrBu[214 N-term,K 214.095357
1889 Xlink:BuUrBu[317 N-term,K 317.158686
1896 Xlink:DSSO[158 K,N-term 158.003765
1898 Xlink:DSS[138 K,N-term 138.06808
1899 Xlink:BuUrBu[196 N-term,K 196.084792
1900 Xlink:DTBP[172 K,N-term 172.01289
1901 Xlink:DST[114 K,N-term 113.995309
1902 Xlink:DTSSP[174 K,N-term 173.980921
1903 Xlink:SMCC[219 C,K,N-term 219.089543
1910 Cation:Al[III D,E,C-term 23.958063
1906 Xlink:BS2G[113 N-term,K 113.047679
1907 Xlink:BS2G[114 N-term,K 114.031694
1908 Xlink:BS2G[217 N-term,K 217.095023
1911 Xlink:DMP[139 K,N-term 139.110947
1912 Xlink:DMP[122 K,N-term 122.084398
1913 glyoxalAGE R 21.98435
1914 Met->AspSA M -32.008456
1915 Decarboxylation D,E -30.010565
1916 Aspartylurea H -10.031969
1917 Formylasparagine H 4.97893
1918 Carbonyl S,R,Q,L,I,E,A,V 13.979265
1922 Pro->HAVA P 18.010565
1920 AFB1_Dialdehyde K 310.047738
1923 Delta:H(-4)O(2) W 27.958529
1924 Delta:H(-4)O(3) W 43.953444
1925 Delta:O(4) W 63.979659
1926 Delta:H(3)C(3)O(2) K 71.013304
1927 Delta:H(4)C(6)O(1) R 92.026215
1928 Delta:H(10)C(8)O(1) K 122.073165
1929 Delta:H(6)C(7)O(4) R 154.026609


Note that some modifications have the same mass as other modifications. These cannot be differentiated by ionbot.

The table below lists the modifications with the same mass (tol=0.02Da):


modification 1 modification 2 abs(mz difference)
N to D DeamidatedN 0.000
A to I TrimethylA 0.000
T to E FormylT 0.000
Q to E DeamidatedQ 0.000
E to Q Glu->pyro-Glu+Methyl:2H(2)13C(1)E 0.005
T to K ethylaminoT 0.000
S to T MethylS 0.000
S to D FormylS 0.000
S to E AcetylS 0.000
S to A DeoxyS 0.000
F to C Phe->CamCysF 0.000
P to E DioxidationP 0.000
F to Y OxidationF 0.000
D to E MethylD 0.000
N to Q MethylN 0.000
N to C MethylthioN 0.000
K to C Lys->CamCysK 0.000
M to T Met->HseM 0.000
N to E Methyl+DeamidatedN 0.000
S to M Delta:H(4)C(2)O(-1)S(1)S 0.000
DethiomethylM Met->HslM 0.000
SulfoY PhosphoY 0.010
G-H2O1K PhosphoguanosineK 0.000
ethylsulfonylethylC BEMAD_CC 0.000
CarboxyethylH EthoxyformylH 0.000
Cation:Ca[II Cation:KD 0.009
Cation:Zn[II Cation:Cu[I 0.008
AA+H2O1-H1O3P1E HydroxyhemeE 0.002
PhosphoCytidineY C-H2O1Y 0.000
SulfoS PhosphoS 0.010
GGX DicarbamidomethylX 0.000
EthylK DimethylK 0.000
PhosphoCytidineS C-H2O1S 0.000
PhosphoCytidineT C-H2O1T 0.000
Cation:Ca[II Cation:KX 0.009
A-H2O1H PhosphoadenosineH 0.000
G-H2O1H PhosphoguanosineH 0.000
PhenylisocyanateX PyridylacetylX 0.000
Cation:Zn[II Cation:Cu[I 0.008
Cation:Zn[II Cation:Cu[I 0.008
Cation:Ca[II Cation:KE 0.009
A-H2O1Y PhosphoadenosineY 0.000
PS_HaptenK ethylsulfonylethylK 0.003
EthylphosphateS O-DimethylphosphateS 0.000
pupylationK C-H1O3P1K 0.000
U-H2O1H PhosphoUridineH 0.000
A-H2O1T PhosphoadenosineT 0.000
O-DimethylphosphateY EthylphosphateY 0.000
SulfoC PhosphoC 0.010
U-H2O1Y PhosphoUridineY 0.000
SulfoT PhosphoT 0.010
PS_HaptenH ethylsulfonylethylH 0.003
PS_HaptenC BEMAD_CC 0.003
A-H2O1K PhosphoadenosineK 0.000
O-DimethylphosphateT EthylphosphateT 0.000
PS_HaptenC ethylsulfonylethylC 0.003
Cation:Zn[II Cation:Cu[I 0.008

What do the search results contain?
  • From the Search Results page you can download your ionbot search result file(s).
    It is recommended to store you result files locally as the ionbot cloud server stores your 10 last projects only.
    This page provides simple descriptive statistics of your search results:
    • Spectra: the number of MS2 spectra that were searched for
    • PSMs: the number of spectra matched at a PSM 1% FDR
    • PEPs: the number of unique peptides (not taking modifications into account) matched at 1% FDR
  • The ionbot result file contains the following columns:
    • scan_id: each spectrum in an MS2 spectrum dataset is numbered with the first spectrum in the dataset having scan_id equal to zero.
    • mz: MS1 mass
    • charge: spectrum charge state
    • matched_peptide: matched peptide sequence
    • modifications: string indicating modifications; the format is "p|m" where "p" is the position in the peptide and "m" is the modification; positions start with position 1 for the first amino acid; position 0 and -1 indicate a modification at the n-terminal and c-terminal respectively.
    • ionbot_psm_score: PSM score computed by ionbot
    • DB: "T" for a match against the target database, "D" for a decoy match
    • unexpected_modification: name of unexpected_modification if matched (a mutation is indicated as X->Y, n-term semi-tryptic peptides are indicated as “semi-tryptic”)
    • ms2pip_pearsonr: MS2PIP b- and y- ion Pearson correlation with observed spectrum (in log2 space)
    • proteins: matched proteins (separated by '||')
    • num_unique_pep_ids: number of unique matched peptides for the protein (only non-shared identified peptides (q-value<=0.01) are counted, value is zero for shared or not-identified peptides)
    • percolator_psm_score: PSM score computed by Percolator
    • q_value: q-value computed by Percolator
    • PEP: Posterior Error Probability computed by Percolator
    • title: spectrum title